In 2013 three whales washed up dead on Japan's shore on the northern tip of Hokkaido. That in itself is not particularly unusual, but these three whales were unlike any that biologists had seen before. 

Was this really a new species of whale, never before officially documented?

They were smaller and darker than the Baird's beaked whale (Berardius bairdii), one of the largest of the 22 species of beaked whale found in the North Pacific Ocean. Were they simply small members of that species, or something else?

Japanese researchers conducted DNA tests. The results hinted at the fact that the three whales might be members of a new species of beaked whale. But the scientist lacked enough samples to make a conclusive case.

Ever since the results of those DNA tests were announced, Phillip Morin of the National Oceanic and Atmospheric Administration (NOAA) wanted to find out more.

Was this really a new species of whale, never before officially documented? He set out to find it.

He had some reason to be optimistic. Locals claimed to have spotted the whale before. They even have a name for it: karasu, meaning crow, or raven, due to its dark hue and diminutive size.

If they do die they are far away from shore and decompose and sink

Even so, Morin’s task was far from easy. Beaked whales are known for their elusiveness.

They spend most of their time far from shore up to 3,000m below sea level, feeding on bottom-dwelling fish and giant squid.

"They are very infrequently seen and they don't wash up on beaches often. If they do die they are far away from shore and decompose and sink," says Morin. 

He, along with a large team of international researchers, identified as many samples of Baird's beaked whales as they could find, from museum collections and rare stranding events.

They obtained a total of 178 that had previously been identified as Baird's beaked whales – and began performing DNA tests.

"I was curious [to see] if we could find other specimens outside of Japan," says Morin. "[Samples] ranged all the way from far western North Pacific in Russia to Mexico." 

This was the proof Morin needed to classify the darker beaked whale as a new species

Combing through the results they found that two of the tissue samples housed in museums matched this new, rare darker whale, currently unnamed but dubbed the "black form" of the Baird's beaked whale.

Along with the three Japanese samples, they found another three that fit the genetic profile. All were shown to be genetically distinct from the Baird's beaked whale, the team write in the journal Marine Mammal Science.

This was the proof Morin needed to classify the darker beaked whale as a new species in the Berardius genus. He now had a total of eight examples. 

This means there are three species in the genus. The "black form" is as different from the other two, the Baird's and Arnoux’s beaked whale – the latter of which is found in the Southern Ocean – as either is from each other. 

Their skin has distinctive oval-shaped scars, evidence that cookie-cutter sharks have nibbled on small chunks of their flesh

"Genetically we could say there was a distinct evolutionary lineage here," explains Morin. "The new species was more similar to the one in the Southern Ocean than it was to the Baird's beaked whale in the North Pacific that it shares the ocean with. 

Unfortunately, this new species has only been identified using samples taken from dead whales. It has never been observed in the wild. For that reason, the black form beaked whale remains elusive.

The team can infer that, like other beaked whales, they are deep divers that spend little time on the ocean's surface. There is indirect evidence that they venture away from the Pacific Ocean to more tropical waters. Their skin has distinctive oval-shaped scars, evidence that cookie-cutter sharks (only found in tropical areas) have nibbled on small chunks of their flesh.

"Beyond that we don’t really know where they range. We still know so little about cetaceans anywhere away from our coast as they are hard to observe and study," Morin told BBC Earth.

"Now that we know it exists, and know a little a bit about it, we can start looking more intensively. There's a lot of curiosity in seeing a new species.

As we learn more and more about them, it becomes even less acceptable to be hunting them in the 21st Century

"Hopefully we'll start documenting them live in the wild, which will help us know where we can find them." 

The differences among beaked whales are subtle, making identifications even trickier. However, one of the study's co-authors, Erich Hoyt, research fellow at Whale and Dolphin Conservation in the UK, says the dark colouring and small size of this new species may make the task easier.

But for this to happen, whaling near Japanese waters will first need to end. "In our study in Kamchatka and especially Bering Island, we're finding that [whales] are highly social with long term relationships between individuals. As we learn more and more about them, it becomes even less acceptable to be hunting them in the 21st Century," adds Hoyt.

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Melissa Hogenboom is BBC Earth's feature writer. She is @melissasuzanneh on Twitter.

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